Paleo Apple Crumb Protein Muffins (Gluten-Free, Dairy-Free, Nut-Free Option)

These Paleo Apple Crumb Protein Muffins with a crumble topping are the perfect solution to an EASY breakfast, snack or lunchbox option that also has protein. Packed with wholesome ingredients like collagen for a protein boost, almond flour for a gluten-free base (see notes for nut-free option!), and warming apple pie spice, these muffins are delicious and great for meal prep. Plus, they’re naturally gluten-free and dairy-free and come with a nut-free option—perfect for anyone with dietary restrictions.

These Protein Muffins are a great way to sneak in extra nutrition for the whole family, making them the ultimate healthy protein snack for breakfast, snack time, or a lunch add-on!

Why You’ll Love These Muffins

• Easy to Make: Simple, wholesome ingredients come together in just a few steps.
• Gluten-Free & Dairy-Free: Perfect for those with food sensitivities.
• Nut-Free Option: Easily swap almond flour for cassava flour for those avoiding nuts.
• High-Protein: Thanks to the collagen or protein powder and eggs, these muffins offer a filling and satisfying protein punch.
• Perfect for Meal Prep: Make a batch ahead of time and enjoy them throughout the week.

Ingredients

• Almond Flour: The base of these muffins, offering a light and tender crumb. If you need a nut-free option, you can easily swap this for cassava flour instead. See recipe notes for details. I prefer “super-fine” almond flour to get the best texture. I like this one from Blue Diamond I can get at Sam’s Club or Amazon. 
• Tapioca Flour: Adds a bit of elasticity and helps bind the muffins together, giving them that perfect muffin texture without any gluten. Though you can use arrowroot or potato starch instead, tapioca is ideal for it’s ability to give a stretch to baked Paleo good that can be dry. Learn more about Paleo flours and how to use them here. 
• Collagen Peptides: The secret ingredient that boosts the protein content, making these muffins not just tasty but also a great source of protein. Yes, you can use another unflavored protein powder of your choice in these as well. There are a lot of collagen brands out there. Use what is most accessible to you. I often get Vital Proteins unflavored collagen when it is on sale at Costco. I love and use regularly BUBS Collagen, which is Whole30 Approved.
• Baking Powder and Salt: Essential for a good rise and to balance the flavors.
• Chopped Apple: Every apple has a different level of moisture and sweetness in it. Use a tart, firm apple like green granny smith apples for this recipe. I finely chop mine in my mini food processor to speed up the prep time. You can peel the apple, but I don’t usually bother!
• Maple Syrup: A natural sweetener that complements the pumpkin perfectly and keeps these muffins refined sugar-free.
• Extra Light Tasting Olive Oil or Avocado Oil: Either of these oils will work well, providing moisture without overpowering the delicate flavors. I usually use extra light-tasting olive oil due to cost. But, make sure it’s “extra light tasting,” not regular olive oil.
• Eggs: They help bind the ingredients together and give the muffins their structure. I do not have a egg-free variation for these muffins. BUT, please leave a comment below if you find one that works well for you, to help others!
• Apple Pie Spice: Because what’s a pumpkin muffin without a warm blend of spices? This adds that cozy, comforting flavor that makes these muffins irresistible. Can’t find a apple pie spice at your store? Make your own with an easy recipe like this one. 

Instructions

Step 1: Prep Your Oven and Ingredients

Start by preheating your oven to 375°F. Line a muffin tin with paper liners or grease well with oil to ensure your muffins come out smoothly.

Step 2: Mix the Dry Ingredients

In a medium bowl, whisk together the almond flour, tapioca flour, collagen or protein powder, baking powder, salt, and apple pie spice. These dry ingredients are what give your muffins the ideal gluten-free texture and that cozy apple pie flavor.

Step 3: Stir in the Wet Ingredients

In another bowl, whisk together the maple syrup, oil, and eggs until well combined. Pour the wet mixture into the dry ingredients and stir until fully mixed. The batter should be thick but still easily spoonable. Gently fold in the finely chopped apples.

Step 4: Make the Crumble Topping

For the crumble topping, combine the almond flour, maple syrup, oil, and apple pie spice in a small bowl. Mix until it forms a crumbly texture, perfect for sprinkling over your muffins. This adds a satisfying, crunchy layer to each bite!

Step 5: Fill and Bake

Spoon the muffin batter into the prepared muffin tin, filling each cup all the way full. Top each muffin with a generous amount of the crumble mixture.

Bake in the preheated oven for 30-35, or until the tops are solid to the touch. Let the muffins cool in the tin for about 5 minutes before transferring to a wire rack to cool completely.

Paleo, Protein-Packed, and Perfect for Any Diet

These Gluten Free Protein Muffins aren’t just for those following a paleo diet; they’re also great for anyone looking to enjoy healthy protein snacks without sacrificing flavor or texture. With options to make these nut-free and dairy-free, this recipe is perfect for sharing at family gatherings, school lunches, or post-workout snacks.

Nut-Free Option

If you or someone in your family needs a nut-free option, simply substitute the almond flour with cassava flour. This easy swap making these muffins safe for nut-free diets. See recipe notes for exact amounts and details.

Storage Tips

These muffins store beautifully. Keep them in an airtight container at room temperature for up to 4 days, with a paper towel underneath them and on top of them to absorb moisture, or in the fridge for up to a week. They also freeze well—just pop them in a zip-top bag, and they’ll stay fresh for up to 3 months. Simply thaw at room temperature or warm in the microwave before enjoying.

Final Thoughts

These Paleo Apple Crumb Protein Muffins with crumble topping are a fantastic way to enjoy the flavors of fall in a healthy, gluten-free, and dairy-free form. Whether you’re looking for a protein-packed snack or a healthy muffin option to enjoy with your morning coffee, these muffins are a perfect choice. With their moist, tender crumb and sweet apple flavor, they’re sure to become a new favorite in your household. Feel free to make them on repeat!

Paleo Apple Crumb Protein Muffins

Autumn @wholefoodfor7

An EASY fall Paleo breakfast or snack favorite filled with 16 grams of protein. Soft, with a tasty crumb topping = sure to be a family hit!

5 from 3 votes

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 30 minutes mins

Total Time 45 minutes mins

Course Breakfast, Snack

Cuisine American

Servings 12 muffins

Calories 344 kcal

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Ingredients

 

Muffins

• 3 cups almond flour (see notes for nut-free)
• 1/2 cup tapioca flour
• 1/2 cup unflavored collagen powder or protein powder
• 2 teaspoons baking powder
• 2 teaspoons apple pie spice
• 1/4 teaspoon salt
• 1/2 cup maple syrup
• 1/4 cup light tasting olive oil or avocado oil
• 2 large eggs
• 2 cups finely chopped or grated green apple

Crumb Topping (optional but recommended)

• 1/2 cup almond flour (see notes for nut-free)
• 2 tablespoons tapioca flour
• 1 pinch salt
• 1 tablespoon maple syrup
• 1 tablespoon light tasting olive oil or avocado oil, melted butter or ghee

Instructions

 

• Start by preheating your oven to 375°F. Line a muffin tin with paper liners or grease well with oil to ensure your muffins come out smoothly.
• In a medium bowl, whisk together the almond flour, tapioca flour, collagen or protein powder, baking powder, salt, and apple pie spice.
• Add the maple syrup, oil, and eggs until well combined. Gently fold in the finely chopped apples.
• For the crumble topping, combine the almond flour, maple syrup, oil, and apple pie spice in a small bowl. Mix until it forms a crumbly texture.
• Spoon the muffin batter into the prepared muffin tin, filling each cup all the way full (about a 1/4 cup of batter each). Top each muffin with a generous amount of the crumble mixture.
• Bake in the preheated oven for 15 minutes, then without opening the oven, reduce heat to 350 degrees and bake another 15 minutes, or until the tops are solid to the touch. Let the muffins cool in the tin for about 5 minutes before transferring to a wire rack to cool completely.
• Keep them in an airtight container at room temperature for up to 4 days, with a paper towel underneath them and on top of them to absorb moisture, or in the fridge for up to a week.
• TO FREEZE: Freeze in a single layer until frozen, then store them in a sealed zip top bag or container for up to 3 months.

Notes

GLAZE: Want to drizzle some glaze on top (pictured)? They don't need it, but the glaze looks beautiful and is fun. I whisked together:

• 3 tablespoons of heavy vegan cream or canned unsweetened full-fat coconut milk (can use other non-dairy milk, it will just be thinner)
• 1 cup powdered sugar or powdered monk fruit sugar
• 1/2 teaspoon vanilla for an easy glaze drizzle.

Put in a sandwich zip top bag, cut off a corner, and use that to drizzle.

NUT-FREE: I prefer the awesome texture of the almond flour + tapioca flour. But, if you need nut-free, use just 1 1/2 cassava flour instead of the almond + tapioca flour. Yes, only 1 1/2 cups cassava flour total (don't use the tapioca flour). Cassava flour is VERY dense and a little goes a long way! Be sure to fluff your cassava flour with a fork prior to using and spoon (don't scoop!) the flour into the cup to prevent over measuring. If your cassava flour muffins turn out dense and dry, you probably accidentally over-measured and used too much. This will only make 9 muffins.

Nutrition

Calories: 344kcalCarbohydrates: 26gProtein: 16gFat: 22gSaturated Fat: 2gPolyunsaturated Fat: 1gMonounsaturated Fat: 4gSodium: 154mgPotassium: 60mgFiber: 4gSugar: 12gVitamin A: 12IUVitamin C: 1mgCalcium: 128mgIron: 2mg

Keyword breakfast, dairy-free, easy, gluten-free, kid-friendly, nut-free, paleo

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